A Wolf in Shepard's Clothing
by KillerGypsyFish
Summary: Noble Six is struggling to get to the rally point to deliver Cortana to Captain Keys, but when the wounded spartan passes out and awakens on some sort of spacecraft. He discovers that he's in a reality where the UNSC don't exsist. Will he get back to his reality? Will he make nice with the crew? And what happened to Cortana? Based off of Kyurem's Soul's, Involuntary Intrusions.
1. Chapter 1

**Somewhere on Reach - 2552**

"Lone Wolf", the name given to the operation Noble 6 was tasked with completing, truth was the young Spartan was anything but a "Lone Wolf". Without his team he felt lost, alone in a world that was about to be glassed by the Covenant. "Lone Wolf", it was like his superiors were rubbing it in his face, he was the only surviving member of Noble team, and he had to complete the mission that the rest of his squad died trying to complete; deliver the A.I. core which held Cortana to Captain Keys. This task seemed easy enough on paper, but in reality the length and complexity of this task was greater than anyone could have expected. One by one Noble fell, Six watched every one of them die, either sacrificing themselves for the good of humanity or taking a bullet right in front of him, he watched them all burn. And now in a desert village on the way to rendezvous with Captain Keys, it was his turn. Bloodied and bruised he limped his way from cover to cover, building to building, trying to escape the endless hoards of Covenant Sangheili elites, but he was growing weak. He knew if he had any chance of making it to the rally point, he would have to find another way. When an opening showed in Covenant defenses, Six plucked weapons from the hands of fallen elites, and pushed forward. However, this opening didn't last long, and soon more Covenant were attacking, surrounding him from every possible angle. Six was becoming sloppy, and he knew it. Time was running out. While moving he used his shotgun to pick off closer targets. He was focusing all to well on the targets, but not on where he was going. Then he hit it, ran square into a wall, knocking him right on his ass. He looked around dizzied, trying to find his barrings. He looked up to find not a wall, but a Sangheili Zealot, silhouetted by one of Reach's many suns. The Zealot's energy sword pulsed in its hand, it paused for a second, let out a gut retching roar, and stomped on Six's left arm, before stabbing him in the abdomen.

When Six came to, he was lying right where the Zealot had stabbed him, in the middle of a now abandoned desert village. His amour's shields took most of the force of the sword, but it still pierced the amour. According to his HUD readout, he was critical with a broken leg, his crushed left arm, and several broken ribs, but luckily for him his ribs stopped the sword from piercing anything vital. Realizing his situation Six layed back, and just listened. Unfortunately, the only sound to be heard was the faint wurring of the Covenant fleets as they began to glass the planet. The once Covenant populated village he was in the middle of was now deserted, nothing but ammo and fallen Covenant remained. "They don't even have the decency to bury their own men." Six hissed, as he spat blood on his visor. Then he remembered his mission, he remembered Cortana. He rolled a bit on his left side, so he could reach the A.I. core that was still attached to the magnetic holster on his lower back. He pulled the core from its holster, and held it in front of him. "Well, if I'm gonna go out, I might as well see if she's in here." Six opened the side of A.I. core. Six being a Spartan, bred for battle, was unaware of the several dozen checks of the core that had to be done, or the mental training, and stimulation that have to be done before noral implantation of an A.I. could take place. Failure of these procedures could result in serious mental and physical injury or death to both the patient and the A.I. But since Six didn't know this he took the small chip that held the A.I. Cortana inside, lifted his head, and slipped it into the small port in the back of his helmet. Almost immediately, he felt like a dozen flash bangs were set off within six inches of his eyes, he felt a headache so bad it felt like his head was going to explode. "Ahhhhhhhhhhh!" An oddly feminine voice screamed. Then nothing, everything went black.


	2. Chapter 2

**Aboard the Normandy – 2186**

"You've got to be kidding me!" A very annoyed Joker exclaimed. He was has frantically flipping switches, press buttons, and occasionally hitting the console.

"Jeff, it appears that the majority of onboard systems have shut down, backup power has come online, but I still have limited control. I will try and run diagnostics to figure out the source of the problem, while finding possible solutions." Exclaimed EDI, the onboard A.I. that had recently transferred part her onboard self in a fully functioning robotic body. This allowed her continue to monitor the Normandy's systems and crew, but also allowed her to be combat ready if need be.

"Thanks, and while you're at it could you call the Commander down here? She'll want to know why we've stopped." Joker replied still messing with the console trying to jump start the thing back to life.

"Unfortunately Jeff, the comms are one of the systems that were shut down. However, there is not a need to communicate with Commander Shepard as she is correctly in the CIC, and heading towards the bridge." EDI stood up to greet Shepard as she walked toward them. "Commander, we are experiencing some type of power failure. We are not sure what is causing it, but it has shut down most of the systems, these include the weapon systems, navigations, communications, and the main engine. Beyond those we're not sure." EDI turn back and sat down in her co-pilot seat. "I'm running several different diagnostics to find the source of the power failures, but nothing has come up yet." She started to type away at her console.

"Well, keep me posted, I'm going to check on the rest of the crew." Commander Shepard said as she turned to walk away.

EDI continued to type into her console when she noticed something. "Wait, Commander. It appears that some of the Normandy's systems are coming back online, but the navigational systems as well as the main engines are still offline."

"Ah, Commander? You're gonna want to look at this." Joker said questionably. He pointed to one of the many monitors on the bridge. However, instead of showing flight paths, diagnostics, or statistics, this monitor was camera footage. "This is one of our cameras in the A.I. core"

The monitor showed the main engine, but something was odd, tangled in the mass of the wiring was a large figure obscured by the smoke. Commander Shepard leaned in closer to try and get a better view of the monitor.

"Stole away perhaps?" She asked.

"Unlikely." EDI's synthetic, but oddly cute voice cut it. "My sensors indicate that the individual is mechanical, although I'm also picking up a faint heartbeat. Most likely, the individual is organic, but is wearing a full body suit similar to yours."

"Well, if this guy's armed I want people down there, now!" Shepard ordered with a much more stern voice than before.

"Shepard, it appears the individual is unconscious, possibly wounded. I recommend that Liara should be in the team heading down, so she can provide medical attention on site, if need be."

Shepard hesitated, "since when did EDI give recommendations about people in certain squads?" She thought to herself, "but she is right, having an Asari go down would be a good idea."

Shepard turned back to EDI. "Acknowledged." She repied. "Have Liara, and Garrus meet me outside the A.I. core." She turned and started jogging back down the bridge. "And let me know if anything changes!" Shepard shouted over her shoulder as she left the bridge.


	3. Chapter 3

Noble Six begrudgingly opened his eyes. He looked around to find that he was in a circular room with metal panels for walls, and a huge engine like object in the center, with a platform leading up to it. He saw that he was in a tangled mess of large cables that were about a foot in diameter, and ran from the wall and into the engine. Six tried to move around to free himself, but was met with excruciating pain from the right side of his chest. "Damn." He staggered as he choked on some blood. Noticing that the wires he was trapped in were pulsing with a bright blue color he remember about Cortana. Trying to reach his back was to painful, giving up he leaned his head back against one of the cables. As he round his head over to one side he saw it, the A.I. core, but something was wrong, the core wasn't glowing. Then Six remembered that he had put the clip into his helmet. Using his still usable right arm, he slowly reached behind his head and felt for the port. His fingers snagged on the surprisingly empty slot. "Where?" He wondered aloud. His eyes turned from the dull, empty core, and onto the still pulsing cables. "Cortana?" He wondered again. This time though, his train of thought was derailed as he heard voices behind the door on the other side to the room. Six tried to reach for his magnum, but it was just out of reach. "Maybe they won't be hell-bent on killing me." Six sarcastically muttered to himself. "Maybe they'll help m-." Six was cut off by the door opening, and three armed figures entered the room, as if they were making sure it was clear. The first figure was a human female. The other two figures, a male and a female, were obviously alien, but Six had never seen either race before. The female had bright blue skin, and had hair that looked like thick tentacles that ran toward the back of her head. The male was much larger, and had a face that had similar characteristics to a light tree bark. They all wore armor similar to his, but without helmets. After they were satisfied with their search, they focus their attention towards the wounded Spartan. The human approached him, walking slowly, gun still in hand.

"Who are you?" She asked insistently, making her way off the platform, and into the cables. Six struggled to reply as it was becoming difficult for him to breath, his helmet was beaten so badly it was no longer venting air in and out of the amour. He raised both arms back over his head, grabbed either side of the helmet twisted, and pulled. This action caused him to wince in pain, as he had forgotten about his broken arm. After freeing the helmet, he used his right arm to toss it beside him. Turned to spit the blood from his mouth, and answered.

"SPARTAN-B312 of Noble team, ma'am." He coughed, still choking on blood. "And you are?"

The woman seemed shocked that Six didn't know who she was.

"I'm Commander Shepard of the Alliance, and you're on my ship. So if you don't mind me asking, what are you doing here?"

"Well that…" He spat again. "I don't rightly know." He chuckled abit, as he spit up even more blood. "So, can I get some medical attention here or what?"

"My apologies. I just have to make sure you're a friendly, that's all." Shepard turned back toward the blue alien. "Liara, can you help patch him up enough, so we can take him to the Med bay?"

The blue alien jogged over to Six, punched something into a holographic tool around her wrist.

"Here, this will help with the pain." She reassured. "Garrus, come help me take him over to the Med bay." The other alien ran over to help Six to his feet, and other to the platform, where a stretcher was waiting. Six could tell that the one that called herself Commander Shepard, was questioning him on the stretcher as they moved through a brightly lit corridor, but he couldn't tell what she was saying, his hearing had become muffled, and his vision blurred, than nothing, just blackness.


	4. Chapter 4

Six awoke to find himself still armored, except for his helmet, and laying down on what looked like a fancy hospital bed. He sat up expecting searing pain, but there was none. He swung his legs over to the right side of the bed, he noticed that there was not a single person in the room. Examining the room, he saw two other beds on the other side of the room, and different types of equipment all around the room. Six stood up and slowly walked over to a door on the far side of the room. The door resembled a kind of blast door, and had a green holographic lock in the center. "You know Noble Six, you really have a habit of falling unconscious, don't you?"

Six quickly spun around, at the same time he reached for his magnum, but found that it wasn't on its magnetic holster. Six was surprised to see a luminescent blue, feminine figure standing the bed his had occupied. She had her arms crossed as she gracefully stepped towards him.

"Cortana?" Six asked, puzzled as for how she was still alive, and able to project herself without a means of projection. "How are you…"

"Alive?" She said, finishing his question. "The very same moment you put the clip I was stored on into your helmet, something happened, a massive surge of electricity perhaps, but I'm not quite sure. This event caused the clip to get severely damaged, and instead of having me die, it put me in the next best storage unit it could find." She raised he hand, and tapped the side of her head with a finger. "It fused me with your consciousness. I'm sorry, but you're stuck with me Noble." She turned towards some of the monitors projecting medical information. "Unfortunately, since I'm fused with your consciousness, I can't project myself through the usual objects, so you're the only person that can see me, but I can still interact with technology."

_"__Great, now I'm stuck with an A.I. stuck in my head. That's just great" _Six thought to himself.

Cortana turned and moved towards Noble Six.

"Oh and I almost forgot. Since I am fused with your consciousness." She stopped and looked him straight the eyes. "_I heard that."_ She said without moving her lips.


	5. Chapter 5

Noble Six was sitting on one of the hospital beds, it had been hours since he had woken up, and no one had entered the med bay. He turned his wavering attention towards the blast door on the far side of the room. In the center of the door was a green holographic lock, Six was familiar with holographic locks, before he joined Noble team lock picking was a valuable skill. It got him out of some sticky situations without being spotted. "_Worth a shot._" He thought to himself. He approached the door, and saw his helmet. The visor was smashed, and the top had been partly dented in, but he picked it up anyway and held it under his left arm. As he got closer to the door, he saw a blue shimmer in his peripheral vison, as Cortana materialized beside him.

"You do know how risky this is." She said, trying to talk him out of it. "Where are you going to go once you get the door open? That is, if you can even open it without setting off any alarms." She walked backward matching his speed.

"Look, if you want to sit around and wait for answers that's fine, but I'm done waiting." He said, as he reached the door. "Let's see if I've still got if." He touched the green glowing panel, expecting a dial of some sort to form around the panel. And was shocked as the door slid open.

"Maybe, I'm a lot better than I thought." He said sarcastically. Stepping out of the med bay, he saw some of the crew of the Normandy siting around a dining area.

"So, the sleeping giant awakes!" He heard one cabin mate yell. "The Commander's gonna want to see you. Head up to the CIC, she'll probably be there. Elevator's just down the hall." Six began walking past the dining area.

"_They're really trusting of me. Shouldn't they be questioning my being here?_" He thought as he walked. "_Well, I guess having a Spartan show up unannounced is kind of expected. Usually the marines are just glad to see us." _He walked up to the elevator door and noticed that there was another green holographic lock. "_Maybe this facility uses these as door knobs and not just locks_. _Unusual, but it could have its uses_." He pressed on the holographic panel, and the door opened, stepping into the elevator, he pressed the button labeled "Command Information Center". "Cortana, you there?" He asked.

"_Of course I'm here, I'm in your head, remember? And you don't need to talk, just think."_

_"__Right, I'm going have to get used to this 'always in my head' thing. I was wondering if you knew anything about this Commander Shepard, because I've never heard of her before." _He turned to his side, expecting to see her beside him, but there was just the metal wall.

"_She does not appear in my records of the UNSC, neither does this vessel the Normandy. However, it is possible that she is working in ONI, they tend to keep their personnel files off the record. It would explain…" _She was cut off by the elevator door sliding open. Six walked forward, stepping into a room that looked similar to a war room, with a holographic map in the center, with a small walkway running up to it. Sure enough, Commander Shepard was right beside the walkway, chatting with another member of the crew. This crew member was also human, she had more of a tan than the Commander, big brown eyes, and short brown hair that just barely touched her back.

"Commander." She said with a British accent, while tilting her head in Noble's direction.

Recognizing she was his superior, the Spartan Lieutenant quickly raised his arm in salute.

"SPARTAN-B312 of the U.N.S.C. reporting for duty." He had stiffened his whole body making him look like a statue. The Commander looked puzzled, as if she was not sure what to make of him. After a few seconds pause, she raised her arm in salute.

"At ease." She said, as they both lowered their arms. She looked him up and down, still with a somewhat puzzled look on her face. "You mentioned your rank before, though I'm not familiar. And this 'U.N.S.C' you speak of, is that a branch of the Alliance?" Noble Six was taken aback by this question.

"_How could someone not know of the U.N.S.C., I'm sure I guess if you've been hiding under a rock for a few decades you could not know what a Spartan is, but the U.N.S.C.? How is that even possible?" _He didn't even know what to say, the U.N.S.C. has literally existed for centuries, for someone to not know at least** of**the U.N.S.C. would be like a Spartan not knowing what the Covenant was. It was just absurd, impossible, inconceivable even. "You know, the U.N.S.C, United Nation Space Command." He said rather resistantly, trying not to insult the Commander's Intelligence. Even so, she was still looking at him confused, befuddled by this information. Six found it hard to believe that a single human being doesn't know about the U.N.S.C., but a Commander? "You're kidding me right? The single military force for the entire human race. The driving force against the Covenant." He paused as if waiting for the Commander to confess to pulling his leg. "Formed four centuries ago in 2163. Seriously, you are joking, right?" Commander Shepard's face had turned from one of confusion to one of anger, not quite rage, but an anger laced with confusion.

"EDI, can you have our guest escorted to the interrogation rooms."

"Wait, what?" Six was stunned that they thought he was insane, after all they're the ones that don't know of the U.N.S.C. Suddenly, two bulky figures were on other side of him. The first of which Six recognized as Garrus, the other was a human male that Six didn't recognize.

"Sorry about this, buddy." Garrus said in his ear. "I was just beginning to like you." Six was preparing to throw Garrus over his shoulder, and simultaneously kick the other soldier in the knee.

"_I don't think that would be wise, Noble."_ Six flinched as he heard the A.I.'s synthetic voice interrupt his thought process. "_Think about it, once you take out these two where are you going to go? You're on their ship, in the middle of space_."

"_So what do_ _you want me to do, just sit here while they drag me off, and interrogate me?"_

_"__For now, yes. Just go along with it. In the meantime, I'll try to figure something else out." _The soldiers began to force Six back into the elevator. _"Wait, I got it. I have a built-in database of U.N.S.C. operations and intel. If I can interact with their computers I can upload and project the files on their monitors. Although, I'm going to need you to distract thing one and thing two before they drag you into the elevator." _Six looked to his left and saw that the other soldier had a flash bang strapped to his waist, just within of reach of his pinned arm.

_"__That shouldn't be too difficult." _He thought, sneaking his hand toward to device. "Hey Shepard." He said, getting her attention as he gently displaced the pin. "If I were you I would close my eyes." He broke free from their hold and dove forward, tucking in and rolling as he touched down. A blinding flash erupted from the elevator, those who were near it covered their eyes in pain, except for Six, Shepard, and the Specialist, who had covered their eyes shortly before the blast. Six stood up and was welcomed to a pistol within three inches of his face.

"You snuck on my ship, insulted my intelligence, made up some bat-shit crazy story about a military branch that I've never even heard of, and now you just blinded two of my men! Give me one good reason I shouldn't put a bullet in your skull right now!"

"This." Six gestured to the monitors just as dozens of files and documented footage about the U.N.S.C. and the Spartan program flashed up on the screens. "I think this proves I'm not as 'bat-shit crazy' as you might think."


End file.
